The swine flu virus, up close (and colorized!)
Credit: C. S. Goldsmith and A. Balish, CDC
Swine Flu has been blanketing the news as of late. On April 29th, the Centers for Disease Control and Prevention (CDC) reported the first US fatality occurring in Texas. The CDC has determined that this swine influenza A(H1N1) virus is contagious and spreading from human to human. Yet at this time, they do not know how easily the virus spreads between people. At our museum, we have taken this very seriously and staff has been asked to stay home if symptoms arise.
CDC is recommending that those who come down with flu-like symptoms stay home from work in order to decrease the rate of infection. The Swine Flu is a viral infection rather than a bacterial infection, which makes it harder to treat. Much of the care for viruses is preventive; viruses are hard to treat after they have entered a living host.
Many people do not know the difference between a viral infection and a bacterial one and consider them interchangeable. Yet they are quite different. Viruses are sub-microscopic particles ranging in size from 20 to 300 nanometers (about 1000 times smaller than the width of a human hair). Viruses must have a living host to function. They remain dormant until they infect a living cell. Within a cell, they then change the genetic material of the cell to replicate the virus. AIDS and Influenza are both created by this process of taking over the normal function of a cell in order to replicate viral cells.
Bacteria do not take over cells. Bacteria are much larger than viruses, usually 10 to 100 times bigger than a virus. Their shapes include curved rods, spheres, rods and spirals. They are known as intercellular organisms because they live between cells. All viruses are harmful to the host because they alter cells, but bacteria can be beneficial (like the species that live in our guts and help us digest our food).
Harmful bacteria in the body create infections like Strep throat or Small Pox. Bacteria can grow and reproduce in both living and non-living environments. Antibiotics are used to treat harmful bacterial growth and infection in the body. Antibiotics; however, are ineffectual against treating viruses.
Because the Swine Flu is a virally spread disease, it is even more important to practice prevention. The CDC sees this disease being spread like a common flu - mainly from person to person through coughing or sneezing by people with influenza. People can also become infected by touching something with flu viruses on it and then touching their mouth or nose. Taking simple precautions like washing your hands and covering your mouth when sneezing is effective prevention. Working in a museum,we take this extra seriously considering how often we come in contact with lots of people and their germs. Many of my co-workers, myself included, have hand sanitizer at our desks, wash our hands often, and carry tissues. It is a simple way to combat an evasive illness.
For more about how to protect yourself from swine flu, check out this podcast from the CDC.
Scientists gather samples on the ocean floor.
Credit: Roger Linington.There's nothing new about looking to nature to cure disease – we've been doing it for thousands of years, with good results. (Two recent examples: The active ingredient in aspirin was first identified in the bark of the willow tree. And we have the Pacific yew tree to thank for one of the strongest anti-cancer drugs out there, Taxol.)
What's different about the work being done at the UC Santa Cruz Chemical Screening Center is that it a) looks to a largely unexplored medical resource: the ocean, and b) uses robots, rather than "forlorn-looking grad students" (to quote Center director Scott Lokey) to run the tests.
Here's a video I shot of one of those robots in action, with Lokey narrating.
One thing that didn't make it into the piece is that these researchers — including Lokey and Roger Linington — aren't just studying every disease they can think of. They focus on the diseases that commercial drug companies tend to neglect because there's so little profit in treating them – things like African sleeping sickness and cholera. So far, they're seeing progress on both, as well as breast cancer.
There is an awful lot of DNA stuffed into every cell.Ben's blog on stars and grains of sand got me to thinking about DNA. How long would the DNA from every living thing on Earth stretch? Could we make it to the next star? The next galaxy? The end of the Universe?
Let's start out with people. Each human cell has around 6 feet of DNA. Let's say each human has around 10 trillion cells (this is actually a low ball estimate). This would mean that each person has around 60 trillion feet or around 10 billion miles of DNA inside of them.
The Earth is about 93 million miles away from the sun. So your DNA could stretch to the sun and back 61 times. That is one person’s DNA.
The best estimate I could find of the world’s population of people is around 6.7 billion. When we multiply 10 billion miles of DNA by 6.7 billion, we end up with, well, a really big number. Something like 6.7 X 1019 or 67 quintillion miles. That is too big a number so let’s convert this to light years.
A light year is around 6 X 1012 miles. So all human DNA would stretch 11.2 million light years. The closest star to Earth (besides the sun) is around 4.2 light years. So we shoot way past that! The Andromeda galaxy is about 2.5 million light years away from us so human DNA could stretch there and back two or three times.
What if we add the rest of the DNA on the planet? It would obviously be much farther but it is hard to calculate because we don’t know how many plants, animals, bacteria, fungi, etc. there are on the planet. We also don’t have detailed information about every species on Earth.
Let's add bacteria to the mix. I decided on this because we know how many cells are in a bacterium—one.
One number I saw was that there are 5 X 1030 bacteria on Earth. Bacterial DNA tends to be a lot smaller than human DNA so there will be less of it per cell. Let's say on average there is 4 million base pairs of DNA/bacterium (this number could be off by a very lot). This translates to around .05 inch of DNA per bacterium which means you need to scrape together around 1.3 million bacteria to get a mile of DNA. So all the bacteria in the world have about 3.5 X 1024 miles of DNA.
How far is 3.5 X 1024 miles of DNA? Well, it is about 640 billion light years of DNA. The end of the observable Universe is about 14 billion light years away. So if we stretched out bacterial DNA it would go to the end of the Universe and back around 23 times. Of course it would be incredibly thin and so actually doesn't take up much space in the Universe.
So that's just human and bacterial DNA. (Well, mostly bacterial since human is so piddly in comparison.) I haven't added all of the rest of the DNA out there. I'll leave that to you.
This photomicrograph shows Cyanobacteria (green) found in a common pond. Image source: Wayne LanierLast blog I talked about mitochondria. These are the parts of a cell that ultimately turn our food into energy. They also have a very interesting past.
A billion years ago or so, mitochondria were free living bacteria. Then our ancestors hijacked them and now they do our bidding. And mitochondria aren't the only cells that got hijacked. So did the chloroplast’s ancestors.
Chloroplasts are the part of a plant cell that turns sunshine into sugar. Every green plant that we’ve looked at has them. And chloroplasts were almost certainly once free living cyanobacteria.
Both mitochondria and chloroplasts still have many bacterial qualities including having their own DNA. But they don't have a lot of their old DNA left. Most of it has migrated to where the rest of our DNA is kept—the nucleus. Or at least that's the theory.
Do scientists have any proof that DNA can move in a cell from compartment to compartment? As a matter of fact they do. At least with the chloroplast.
Scientists used their ability to put DNA specifically into a chloroplast or mitochondrion to design an experiment to look for cells where DNA had migrated. What they did was put some DNA into a chloroplast that could only be read in the nucleus. (Remember, chloroplasts and mitochondria are different enough that nuclear DNA doesn't work there and vice versa.)
The DNA they put in made the plant resistant to a poison IF the DNA could be read. One way the plant could survive was if the DNA they put in the chloroplast ended up moving from there to the nucleus. And it did.
In fact, it was pretty common in their experiment. The DNA moved in something like 1 in 16,000 pollen cells. A rate like this suggests that, for example, different cells on the same leaf might have different amounts of chloroplast DNA in their nuclei.
So DNA can move from the chloroplast to the nucleus. And probably from the mitochondrion to the nucleus too. The evidence is less direct for this but there is plenty of DNA in the nuclei of lots of different plants and animals that looks very mitochondrion-like.
This all fits in with our understanding that DNA is not as stable as a lot of people think. DNA changes between generations and within an organism. Chromosomes can get rearranged, genes copied or deleted, small DNA changes can happen and who knows what else. And these changes are a big part of the motor that drives evolution.
The Mars Science Laboratory. Credit: NASA/JPL-Caltech
When I hear about the search for alien life, it's hard not to think about all the science fiction movies with little green men and Earth-destroying spacecraft. But it's an idea that's far from science fiction for scientists at NASA Ames.
NASA is preparing to send their next rover to the surface of Mars, known as the Mars Science Laboratory. It follows the legacy of the twin rovers Spirit and Opportunity, who have survived far longer than NASA scientists expected. After four years, they're still sending data from the Martian surface. (For an update, check out this post from QUEST blogger Ben Burress).
The Mars Science Lab rover will have a few upgrades, though. It's much larger than Spirit and Opportunity and will be nuclear-powered — meaning no solar cells that are vulnerable to dust storms. It will also be carrying the most advanced lab equipment yet, some of which will look for organic matter on the surface. The goal to discover how habitable the surface could have been for life.
When it comes to what kind of life, it's microbial life that many scientists believe is the best case scenario. There have been a number of recent discoveries that are promising evidence that liquid water once existed on the surface. But if even the conditions were right for life then, they're certainly not right today. Thanks to a thin atmosphere, Mars is bombarded by solar radiation and conditions are dry and cold. Still, many scientists think there's a possibility that life could survive in the subsurface, where it's warmer and more sheltered.
The question most of us would ask, though, is: even if we found extraterrestrial life someday, how would we recognize it? NASA scientist Chris McKay explained his take to me. It turns out there are some basic things scientists believe they could look for. You can hear what he has to say in this audio clip:
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McKay brought up another interesting point — we've already sent earthlings to Mars. The NASA rovers were built in clean rooms, but they're not completely sterile. Chances are there are microbes from Earth on Mars now, protected inside machinery we built. McKay believes this contamination is reversible, and there's already a policy in place to protect both Earth and Mars known as planetary protection. You can hear McKay explain why it's so important in this clip.
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No matter what the outcome of the Mars Science Lab mission, there's a lot more to discover about what Mars is like today and about its past.
We put this story on the calendar back in September, before melamine-tainted milk started making headlines in China (with some products turning up on Asian grocery store shelves here in the US. Find KQED reporter Oanh Ha's excellent reporting on that story here, here, and here). We'd been planning to focus on criticism of FDA's handling of imported fresh produce, and had to recast the piece when it became clear that the concerns around food safety were much broader.
Another plan was shelved when the FDA declined to let us visit any of their local facilities, including a testing lab in Alameda that had been scheduled for closure only a year ago – right around the time that Mexican jalapeno peppers sickened 13,000 people and devastated the domestic tomato industry. (Officials blamed tomatoes before narrowing in on the peppers.) Luckily, the press office from the Bureau of Customs and Border Patrol generously agreed to show us around a Port of Oakland warehouse, where –- I quickly discovered — there were no FDA inspectors to be found. That's because FDA inspectors do their Port work largely in front of computer screens, scanning shipping manifests for products they believe warrant physical inspection.
That means two things: One, the FDA relies largely on the exporters' own description of what's in the product. As several people told me, it's an "honor system." Two, almost none (less than one percent) of the imported produce is ever tested for salmonella, e.coli, or any of the other human health threats we worry about.
When we finally talked to FDA Director of Food Safety David Acheson by phone from Maryland, he made the point pretty clearly: FDA knows its food safety program needs work. But that's going to require more and sustained funding. It'll be interesting to see how well the agency can make that case come January.
Unless our sewage happens to end up in the Bay and in the headlines, most of us probably never give a second thought to where our wastewater is headed each time we run the tap or flush the toilet.
To learn more about the travels of sewage, I took a tour of the Las Gallinas Valley Sanitary District treatment plant led by Plant Manager Matt Pierce. The plant has been in operation for about 50 years and serves over 30,000 residents in north San Rafael.
After leaving sinks and showers throughout the District, wastewater travels through a network of pipes and pump stations. Once the sewage arrives at Las Gallinas, it passes through an inlet screen and a grit chamber, which together remove much of the dense, inorganic material-"like diamond rings," Matt jokes.
A lot of what happens at the plant is not that different from what happens in your compost pile: "It's basically bacteria at work," Matt points out. (The much bigger challenge for sanitation districts these days are all the unnatural things we're putting down the drain: household chemicals, personal care products, pharmaceuticals.)
From the grit chamber the sewage heads into a series of clarifiers, where gravity causes the organic solids to settle out. The biosolids pass through a thickener and then an anaerobic digester-the most, ahem, aromatic stop on our tour. After further thickening in storage ponds, the sludge is injected into a disposal field.
Meanwhile, the liquid from the clarifiers travels through two biofilters, where rotating arms spray the water over rock beds. The organic matter in the wastewater is a feast for microbial slime living on the rocks. In the nitrification tower, more microorganisms break down the ammonia in the water. In the final stages of treatment, the wastewater is chlorinated to kill any remaining bacteria, then dechlorinated since the chlorine is toxic to many aquatic species. Finally, the treated water is sprayed onto District fields or discharged into Miller Creek where it flows to San Pablo Bay.
The District has done a lot to minimize the environmental impacts of its operations. The plant is powered by a field of solar panels. The methane released in the sludge treatment process is captured and used to generate power and heat the digester. Some of the treated wastewater supports acres of fresh and saltwater wetlands-in fact the District's land is a favorite local gem for walkers and birders. And in a partnership with the Marin Municipal Water District, more than a million gallons of treated wastewater are recycled daily for landscape irrigation and other projects.
There are plans to make even fuller use of the reclaimed water. The Bay Institute-in partnership with the Sonoma County Water Agency, Las Gallinas, and three other North Bay sanitation agencies-has developed a plan to use recycled water for wetland and creek restoration and for agricultural irrigation. Legislation sponsored by Congressman Mike Thompson to establish the program passed the House late last year; Senator Dianne Feinstein has introduced similar legislation that we are hopeful will pass this year.
With California's growing demands for water, such creative means to conserve and recycle are critical to helping prevent this precious resource from just going "down the drain."
Ann Dickinson is Communications Manager for The Bay Institute (www.bay.org), a nonprofit research, education, and advocacy organization dedicated to protecting and restoring San Francisco Bay and its watershed, "from the Sierra to the sea."
If Chicago has deep dish pizza and Boston has cream pie, San Francisco has sourdough bread. And just like the pizza and pie, San Francisco sourdough just isn't the same outside its hometown.
But that's because only San Francisco is home to a certain bacterium that bears its name– Lactobacillus sanfranciscensis.
Of course bread uses another microbe– the yeast that turns sugar into the air bubbles that lighten the loaf. For sourdough, though, local bacteria then add their secret ingredient. They eat up the yeast's waste and turn it into acid, making the bread San Francisco sour.
The bacteria also make the dough inhospitable for other microbes, keeping all that doughy goodness for the yeast and itself. The yeast and bacteria make such great partners because the yeast can't eat the sugar maltose, which the bacteria absolutely need.
San Franciscans have been noshing on this local concoction since at least the Gold Rush. Boudin Bakery first baked buns in 1849. Some bakeries even claim to have a "starter"– the bit of dough that contains yeast and bacteria– that's over a century old. They pinch off a piece of starter for every new loaf, and care for the dough with regular feedings of flour and water.
If you've got a favorite brand, chances are it's because of the unique mix of yeast and bacteria from that bakery. Other towns' sourdough will taste a little bit different because their bacteria aren't the San Francisco kind.
Want to whip up a loaf unique to your backyard? The Exploratorium has a recipe to make your own starter that will pick up local yeast and bacteria. Or if you prefer that authentic San Francisco flavor, buy the original.
The QUEST Community Science Blog explores local science, nature, and environment issues & experiences in Northern California. A collaborative effort, our many writers come from local museums, zoos, science centers and research institutions, as well as KQED's TV and Radio producers covering stories in the field.
The swine flu virus, up close (and colorized!)
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There is an awful lot of DNA stuffed into every cell.
This photomicrograph shows Cyanobacteria (green) found
Amber Dance is the Quest Intern and a